An accurate mass can narrow the list of candidate compounds while leaving multiple structures possible. In a fungal metabolite study, Clevenger and colleagues found one mass-to-charge value at two different retention times. They suspected two related forms of benzomalvin.
The proposed formula agreed with the observed neutral mass within one part per million. That agreement supported the candidate formula. The researchers then synthesized a reference containing benzomalvin A and D and compared it with the fungal extract by liquid chromatography–mass spectrometry. The comparison included injecting the standard together with the extract. The authors used those observations to confirm their assignment of the two peaks.
Separate the evidence for elemental composition from the evidence that distinguishes closely related compounds. Look at which reference material was used and which properties agreed, such as retention times and mass-spectral features. This was a fungal biosynthesis experiment. Its workflow illustrates chemical identification, while the performance of a method in another sample type would require separate evidence.
Clevenger et al., Nature Chemical Biology (2017), full text · DOI